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METABASE Ontology

Contents:

Class Hierarchy


Class Definitions

This section of the HTML version of the ontology contains the class definitions of the ontology. Each class defines a type of entity. A class is defined to have a set of slots, where each slot defines attributes and properties that may be used by an instance of that class.

Slots are inherited by a class from its parent classes. Usually this HTML form of the ontology shows only the names of the slots at each class, with links provided to the full definition of the slot in the slot section of the ontology. However, when the definition of a slot is changed within a class with respect to its parent, the full definition of the slot is shown.

Class: Databases

Superclasses: FRAMES

Instances: SGD-PATHWAY, ECHOBASE, PIRE, UNIPROT, CAS, NCBI-TAXONOMY-DB, ECOCYC, ECOGENE, BIOHEALTHBASE, UCSC, DBGET, UM-BBD-CPD, PUBCHEM, CGSC, ECOL199310CYC, WIT-PWY, PDB, MTBCDCCYC, HOMINISDB2, ENTREZ, GENECARDS, WIT, NRSUB, LIGAND-CPD, OU-MICROARRAY, SWISSPROT, NCI, ECOO157CYC, REFSEQ, TAIR, LIGAND, SHIGELLACYC, NCBI-GENE, LOCUSLINK, PUBMED, METACYC, UM-BBD-PWY, PYLORIGENE, MTBRVCYC, GO, SOYBASE, PID, UNIGENE, SWISSMODEL, SFLE198214CYC, SGD, ENZYME-DB, MIM, LIGAND-MAP, NEW-WIT-PWY, MPMP, HIDB, ENSEMBL, COLIBLAST, ECOLIHUB, CRYPTODB, HOMINISDB, CYRPTODB, ASAP, PFAM, HUMANCYC, PLASMOCYC, ECOLIWIKI, MODBASE, Wikipedia, CHEBI, BRENDA, ARACYC, INTERPRO, GI, KNAPSACK, REACTOME, SGN, PIR

Slots:

Instance Definitions

Instance: SGD-PATHWAY

Types: Databases

Slots:

Instance: ECHOBASE

Types: Databases

Slots:

Instance: PIRE

Types: Databases

Slots:

Instance: UNIPROT

Types: Databases

Slots:

Instance: CAS

Types: Databases

Slots:

Instance: NCBI-TAXONOMY-DB

Types: Databases

Slots:

Instance: ECOCYC

Types: Databases

Slots:

Instance: ECOGENE

Types: Databases

Slots:

Instance: BIOHEALTHBASE

Types: Databases

Slots:

Instance: UCSC

Types: Databases

Slots:

Instance: DBGET

Types: Databases

Slots:

Instance: UM-BBD-CPD

Types: Databases

Slots:

Instance: PUBCHEM

Types: Databases

Slots:

Instance: CGSC

Types: Databases

Slots:

Instance: ECOL199310CYC

Types: Databases

Slots:

Instance: WIT-PWY

Types: Databases

Slots:

Instance: PDB

Types: Databases

Slots:

Instance: MTBCDCCYC

Types: Databases

Slots:

Instance: HOMINISDB2

Types: Databases

Slots:

Instance: ENTREZ

Types: Databases

Slots:

Instance: GENECARDS

Types: Databases

Slots:

Instance: WIT

Types: Databases

Slots:

Instance: NRSUB

Types: Databases

Slots:

Instance: LIGAND-CPD

Types: Databases

Slots:

Instance: OU-MICROARRAY

Types: Databases

Slots:

Instance: SWISSPROT

Types: Databases

Slots:

  • BASE-URL: http://www.expasy.ch/sprot/sprot-top.html
  • COMMENT: Technically, Swiss-Prot is a subset of UniProt. It is preferable to link using the DBID UNIPROT, because linking via DBID SWISSPROT assumes we know that a protein is in SwissProt as opposed to TrEMBL. DBID SWISSPROT is provided for backward compatibility with earlier BioCyc links that use that DBID. Because even in the existing links it is possible that some links are really to TrEMBL, I have changed the Common-Name slot in this frame to be UniProtKB (PDK).
  • COMMON-NAME: UniProtKB
  • NAMES
  • SCHEMA?
  • STATIC-SEARCH-URL: http://www.expasy.ch/cgi-bin/sprot-search-ac?~A

Instance: NCI

Types: Databases

Slots:

Instance: ECOO157CYC

Types: Databases

Slots:

Instance: REFSEQ

Types: Databases

Slots:

Instance: TAIR

Types: Databases

Slots:

Instance: LIGAND

Types: Databases

Slots:

Instance: SHIGELLACYC

Types: Databases

Slots:

Instance: NCBI-GENE

Types: Databases

Slots:

  • ABBREV-NAME: Entrez-gene
  • COMMENT: The Entrez-Gene Database allows reference to individual genes that were sequenced as part of a genome sequencing project. The accession number of the genes in the database is referred to as a Gene ID. When references to Gene IDs are included in the annotated genome of an organism, the PathoLogic component of Pathway Tools will create links to this database during the generation of the PGDB.
  • COMMON-NAME: Entrez-Gene
  • NAMES
  • SCHEMA?
  • SEARCH-OBJECT-CLASS: Genes, DNA-Segments
  • STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&list_uids=~A

Instance: LOCUSLINK

Types: Databases

Slots:

Instance: PUBMED

Types: Databases

Slots:

  • BASE-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  • SCHEMA?
  • STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=~A&dopt=Abstract

Instance: METACYC

Types: Databases

Slots:

Instance: UM-BBD-PWY

Types: Databases

Slots:

Instance: PYLORIGENE

Types: Databases

Slots:

Instance: MTBRVCYC

Types: Databases

Slots:

Instance: GO

Types: Databases

Slots:

Instance: SOYBASE

Types: Databases

Slots:

Instance: PID

Types: Databases

Slots:

Instance: UNIGENE

Types: Databases

Slots:

  • ABBREV-NAME: UniGene
  • BASE-URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
  • COMMENT: UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
  • COMMON-NAME: NCBI UniGene (Homo sapiens)
  • NAMES
  • SCHEMA?
  • SEARCH-OBJECT-CLASS: DNA-Segments
  • STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=~A

Instance: SWISSMODEL

Types: Databases

Slots:

Instance: SFLE198214CYC

Types: Databases

Slots:

Instance: SGD

Types: Databases

Slots:

Instance: ENZYME-DB

Types: Databases

Slots:

Instance: MIM

Types: Databases

Slots:

  • ABBREV-NAME: OMIM
  • BASE-URL: http://www.ncbi.nlm.nih.gov/omim/
  • COMMENT: This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information.
  • COMMON-NAME: Online Mendelian Inheritance in Man
  • NAMES
  • SCHEMA?
  • SEARCH-OBJECT-CLASS: Genes
  • STATIC-SEARCH-URL: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=~A

Instance: LIGAND-MAP

Types: Databases

Slots:

Instance: NEW-WIT-PWY

Types: Databases

Slots:

Instance: MPMP

Types: Databases

Slots:

Instance: HIDB

Types: Databases

Slots:

Instance: ENSEMBL

Types: Databases

Slots:

Instance: COLIBLAST

Types: Databases

Slots:

  • COMMENT: This is not exactly a database; it is a collection of files that contain blast reports from the comparision of H.inf genes to E. coli genes.
  • COMMON-NAME: ColiBlast
  • NAMES
  • SCHEMA?
  • STATIC-SEARCH-URL: http://www.ai.sri.com/cgi-bin/sb/blast2html.pl.cgi?filename=~A

Instance: ECOLIHUB

Types: Databases

Slots:

Instance: CRYPTODB

Types: Databases

Slots:

Instance: HOMINISDB

Types: Databases

Slots:

Instance: CYRPTODB

Types: Databases

Slots:

Instance: ASAP

Types: Databases

Slots:

Instance: PFAM

Types: Databases

Slots:

Instance: HUMANCYC

Types: Databases

Slots:

Instance: PLASMOCYC

Types: Databases

Slots:

Instance: ECOLIWIKI

Types: Databases

Slots:

Instance: MODBASE

Types: Databases

Slots:

Instance: Wikipedia

Types: Databases

Slots:

Instance: CHEBI

Types: Databases

Slots:

Instance: BRENDA

Types: Databases

Slots:

Instance: ARACYC

Types: Databases

Slots:

Instance: INTERPRO

Types: Databases

Slots:

Instance: GI

Types: Databases

Slots:

Instance: KNAPSACK

Types: Databases

Slots:

Instance: REACTOME

Types: Databases

Slots:

Instance: SGN

Types: Databases

Slots:

Instance: PIR

Types: Databases

Slots:


Slot Definitions

This section of the HTML version of the ontology contains the slot definitions of the ontology. Each slot itself has several properties such as documentation about that slot, a cardinality (specifying the number of values that the slot may have), a value type (specifying the data type of slot values), and a domain (specifying the class(es) in which the slot is used).

Slot NameDocumentationProperties
ABBREV-NAME An abbreviated name for the current frame. This slot can be used for virtually all classes; see specification of the :Synonym-Slots for a given class to be sure. In particular, this name for a database is displayed in DB-links, and in some author credit displays of an organization's name. DOMAIN: Compounds, Organizations, Databases
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
MAXIMUM-CARDINALITY: 1
COMMON-NAME: Abbreviated-Name
BASE-URL Stores URL for Database home page DOMAIN: Databases
VALUE-TYPE: STRING
COMMON-NAME: Base-URL
COMMENT The Comment slot stores a general comment about the object that contains the slot. QUERYABLE?: T
DOMAIN: THING
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
COMMON-NAME: Comment
COMMENT-INTERNAL A comment for internal purposes that is not released to the public. DOMAIN: THING
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
PRIVATE?: T
COMMON-NAME: Comment-Internal
COMMON-NAME The primary name by which an object is known to scientists -- a widely used and familiar name (in some cases arbitrary choices must be made). QUERYABLE?: T
DOMAIN: SLOTS, THING
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
MAXIMUM-CARDINALITY: 1
COMMON-NAME: Common-Name
CREDITS This slot attributes credit to various contributors, which can be individual people or organizations, or both. The type of contribution is indicated by several types of annotation labels that are attached to the slot values, each of them bearing numerical time-stamps as the values (in Common Lisp universal time format) that indicate the approximate times of the contributions. The code dealing with author-crediting sets and shows the timestamps with a precision of one day. The legal slot values are frames of the |People| or |Organizations| classes, in any combination or order. Each such contributor frame is assumed to occur only once in the slot. As of Oct. 2005, the legal annotation labels are: CREATED REVIEWED REVISED LAST-CURATED . For the annotation labels CREATED and LAST-CURATED , it only makes sense to store one timestamp, but for the other labels, in general, arbitrarily many timestamps can be recorded. An association between authors and organizations is assumed if they share the same credit event, in terms of the same combination of annotation label and timestamp. QUERYABLE?: T
DOMAIN: THING
VALUE-TYPE: (OR People Organizations)
INVERSE: CREDITED-FOR
INHERITANCE-TYPE: UNIQUE
COMMON-NAME: Credits
DATA-SOURCE A string describing the data source from which this object was derived, such as the name of a laboratory or a database. Used principally by the PTools BioPAX importer. QUERYABLE?: T
DOMAIN: THING
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
COMMON-NAME: Data-Source
HISTORY Contains a textual history of changes made to this frame. Each item is either a string or a note frame. DOMAIN: THING
VALUE-TYPE: (OR STRING Notes)
INVERSE: REFERENT-FRAMES
INHERITANCE-TYPE: UNIQUE
COLLECTION-TYPE: LIST
COMMON-NAME: History
LINK-PREFIX-TEXT This slot contains an optional string that the Navigator should display before every link to this database. DOMAIN: Databases
VALUE-TYPE: STRING
MAXIMUM-CARDINALITY: 1
COMMON-NAME: Link-Prefix-Text
LOCAL-KB-ORGID The Pathway Tools orgid for databases that are Pathway/Genome Databases (e.g. META for MetaCyc, ECOLI for EcoCyc). DOMAIN: Databases
VALUE-TYPE: SYMBOL
COMMON-NAME: Local-KB-OrgID
NAMES This is a computed slot that returns the union of all names of this frame, by appending names from all other name slots. QUERYABLE?: T
DOMAIN: Polymer-Segments, Organisms, Generalized-Reactions, Enzymatic-Reactions, Chemicals, Databases
VALUE-TYPE: STRING
GET-METHODS: GET-NAMES
READ-ONLY: T
COMMON-NAME: Names
PGDB? True if the database is a Pathway/Genome Database that uses the Pathway Tools schema. DOMAIN: Databases
VALUE-TYPE: BOOLEAN
CARDINALITY: 1
COMMON-NAME: PGDB?
REGEXP This slot contains a regular expression string defining legal values for links to this database. The regular expression syntax is mostly compatible with Perl regular expression syntax, and is described at http://franz.com/support/documentation/8.1/doc/regexp.htm#regexp-new-summary-2. DOMAIN: Databases
VALUE-TYPE: STRING
SCHEMA? This slot is used to indicate which KB classes are logically part of the general GenoPath (MetaCyc) schema (are organism-independent), in contrast to those classes that are specific to a particular organism.

This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring.

The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions.

DOMAIN: THING
VALUE-TYPE: BOOLEAN
INHERITANCE-TYPE: OVERRIDE
MAXIMUM-CARDINALITY: 1
COMMON-NAME: Schema?
SEARCH-OBJECT-CLASS This slot lists the classes of PGDB objects (e.g. Pathways, Genes, Proteins, etc.) that can have unification links to this database via the search URL. DOMAIN: Databases
VALUE-TYPE: THING
COMMON-NAME: Search-Object-Class
STATIC-SEARCH-URL Stores URL format string for OID searches. Format string has one arg: the desired OID. DOMAIN: Databases
VALUE-TYPE: STRING
COMMON-NAME: Static-Search-URL
SYNONYMS One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object. QUERYABLE?: T
DOMAIN: THING
VALUE-TYPE: STRING
INHERITANCE-TYPE: UNIQUE
COMMON-NAME: Synonyms